Table 2.

CAU Characteristics of variants. CAUCASIAN.

CHROM	LOCUS	POS	ID	REF	ALT	A1	A1_CT	ALLELE_CT	A1_CASE_CT	A1_CTRL_CT	CASE_ALLELE_CT	CTRL_ALLELE_CT	CASE_NON_A1_CT	CASE_HET_A1_CT	CASE_HOM_A1_CT	CTRL_NON_A1_CT	CTRL_HET_A1_CT	CTRL_HOM_A1_CT	A1_FREQ	A1_CASE_FREQ	A1_CTRL_FREQ	OBS_CT
1	MTHFR	11794419	rs1801131	T	G	G	630	2172	103	527	374	1798	95	81	11	437	397	65	0.290	0.275	0.293	1086
1	MTHFR	11796321	rs1801133	G	A	A	847	2204	157	690	376	1828	63	93	32	339	460	115	0.384	0.418	0.377	1102
1	PROX1	213985913	rs340874	T	C	T	1065	2206	185	880	376	1830	51	89	48	236	478	201	0.483	0.492	0.481	1103
1	LYPLAL1	219527177	rs2785980	T	C	C	717	2202	107	610	376	1826	96	77	15	396	424	93	0.326	0.285	0.334	1101
1	MTR	236885200	rs1805087	A	G	G	397	2204	54	343	378	1826	137	50	2	600	283	30	0.180	0.143	0.188	1102
2	DPYSL5	26930006	rs1371614	C	T	T	572	2204	111	461	378	1826	87	93	9	521	323	69	0.260	0.294	0.252	1102
2	GCKR	27518370	rs780094	T	C	T	1043	2208	153	890	378	1830	69	87	33	251	438	226	0.472	0.405	0.486	1104
2	MAP3K19	134998059	rs1530559	A	G	A	765	2202	139	626	374	1828	73	89	25	391	420	103	0.347	0.372	0.342	1101
2	RBMS1	160460949	rs6742799	A	C	C	389	2200	62	327	374	1826	130	52	5	618	263	32	0.177	0.166	0.179	1100
2	FIGN	163641436	rs2119289	C	G	C	284	2204	44	240	378	1826	149	36	4	686	214	13	0.129	0.116	0.131	1102
2	COBLL1	164694691	rs7607980	T	C	C	318	2204	41	277	378	1826	151	35	3	655	239	19	0.144	0.108	0.152	1102
2	G6PC2	168906638	rs560887	T	C	T	581	2208	88	493	378	1830	114	62	13	491	355	69	0.263	0.233	0.269	1104
2	G6PC2	168917561	rs563694	C	A	C	679	2194	110	569	378	1816	94	80	15	419	409	80	0.309	0.291	0.313	1097
2	IRS1	226203364	rs2943634	A	C	A	673	2176	112	561	374	1802	88	86	13	424	393	84	0.309	0.299	0.311	1088
2	IRS1	226795828	rs1801278	C	T	T	188	2206	39	149	376	1830	151	35	2	770	141	4	0.085	0.104	0.081	1103
3	PPARG	12348985	rs17036328	T	C	C	205	2208	31	174	378	1830	161	25	3	752	152	11	0.093	0.082	0.095	1104
3	PPARG	12351626	rs1801282	C	G	G	194	2208	29	165	378	1830	163	23	3	759	147	9	0.088	0.077	0.090	1104
3	UBE2E2	23413299	rs1496653	A	G	G	394	2208	62	332	378	1830	135	46	8	611	276	28	0.178	0.164	0.181	1104
3	AMT	49417897	rs11715915	C	T	T	713	2188	128	585	376	1812	83	82	23	422	383	101	0.326	0.340	0.323	1094
3	ADCY5	123346931	rs11708067	A	G	G	359	2192	70	289	376	1816	124	58	6	636	255	17	0.164	0.186	0.159	1096
3	SLC2A2	170999732	rs11920090	T	A	A	352	2204	57	295	376	1828	136	47	5	644	245	25	0.160	0.152	0.161	1102
3	IGF2BP2	185793899	rs4402960	G	T	T	695	2208	148	547	378	1830	68	94	27	441	401	73	0.315	0.392	0.299	1104
3	IGF2BP2	185795604	rs7651090	A	G	G	696	2208	147	549	378	1830	67	97	25	436	409	70	0.315	0.389	0.300	1104
3	ADIPOQ	186853103	rs2241766	T	G	G	400	2206	70	330	378	1828	126	56	7	608	282	24	0.181	0.185	0.181	1103
4	WFS1	6288259	rs4458523	T	G	T	825	2194	140	685	372	1822	73	86	27	361	415	135	0.376	0.376	0.376	1097
4	FAM13A	88820118	rs3822072	G	A	A	1065	2196	189	876	374	1822	43	99	45	230	486	195	0.485	0.505	0.481	1098
4	TET2	105160479	rs9884482	T	C	C	870	2196	142	728	374	1822	75	82	30	319	456	136	0.396	0.380	0.400	1098
4	PDGFC	156798972	rs4691380	C	T	T	827	2204	145	682	376	1828	69	93	26	353	440	121	0.375	0.386	0.373	1102
5	IRX1	4355595	rs17727202	T	C	C	165	2208	27	138	378	1830	162	27	0	779	134	2	0.075	0.071	0.075	1104
5	ANKRD55	56510924	rs459193	A	G	A	663	2208	105	558	378	1830	100	73	16	451	370	94	0.300	0.278	0.305	1104
5	ZBED3	77130042	rs7708285	G	A	G	658	2208	128	530	378	1830	84	82	23	460	380	75	0.298	0.339	0.290	1104
5	PCSK1	96207022	rs13179048	C	A	A	623	2208	99	524	378	1830	102	75	12	454	398	63	0.282	0.262	0.286	1104
5	PCSK1	96295001	rs17085593	C	G	G	637	2204	103	534	376	1828	99	75	14	443	408	63	0.289	0.274	0.292	1102
5	PCSK1	96393194	rs6235	C	G	G	565	2200	88	477	374	1826	107	72	8	481	387	45	0.257	0.235	0.261	1100
6	RRB1	7212967	rs17762454	C	T	T	615	2188	95	520	372	1816	102	73	11	462	372	74	0.281	0.255	0.286	1094
6	RREB1	7231610	rs9379084	G	A	A	332	2208	66	266	378	1830	130	52	7	668	228	19	0.150	0.175	0.145	1104
6	CDKAL1	20679478	rs7756992	A	G	G	549	2192	86	463	374	1818	108	72	7	503	349	57	0.250	0.230	0.255	1096
6	CDKAL1	20686765	rs9368222	C	A	A	522	2206	80	442	378	1828	115	68	6	523	340	51	0.237	0.212	0.242	1103
6	RSPO3	127131790	rs2745353	C	T	T	1075	2206	177	898	378	1828	52	97	40	240	450	224	0.487	0.468	0.491	1103
7	DGKB	15024684	rs2191349	G	T	G	987	2202	175	812	376	1826	56	89	43	286	442	185	0.448	0.465	0.445	1101
7	GCK	44189469	rs1799884	C	T	T	424	2208	77	347	378	1830	119	63	7	599	285	31	0.192	0.204	0.190	1104
7	GCK	44196069	rs4607517	G	A	A	409	2184	74	335	378	1806	120	64	5	597	277	29	0.187	0.196	0.185	1092
7	GRB10	50690548	rs933360	C	T	C	530	2196	91	439	374	1822	108	67	12	523	337	51	0.241	0.243	0.241	1098
7	GRB10	50723882	rs6943153	T	C	T	602	2184	102	500	372	1812	98	74	14	469	374	63	0.276	0.274	0.276	1092
7	HIP1	75546898	rs1167800	A	G	G	974	2208	156	818	378	1830	62	98	29	281	450	184	0.441	0.413	0.447	1104
8	PPP1R3B	9326086	rs4841132	A	G	A	135	2208	22	113	378	1830	167	22	0	809	99	7	0.061	0.058	0.062	1104
8	PPP1R3B	9330085	rs7004769	A	G	A	407	2204	63	344	378	1826	131	53	5	609	264	40	0.185	0.167	0.188	1102
8	ANK1	41651740	rs12549902	G	A	G	1025	2198	175	850	378	1820	54	95	40	238	494	178	0.466	0.463	0.467	1099
8	SLC30A8	117172544	rs13266634	C	T	T	581	2208	98	483	378	1830	104	72	13	485	377	53	0.263	0.259	0.264	1104
8	SLC30A8	117172786	rs3802177	G	A	A	567	2208	95	472	378	1830	106	71	12	490	378	47	0.257	0.251	0.258	1104
8	SLC30A8	117173494	rs11558471	A	G	G	601	2206	99	502	378	1828	103	73	13	466	394	54	0.272	0.262	0.275	1103
9	GLIS3	4287466	rs7041847	A	G	G	1034	2202	167	867	376	1826	63	83	42	245	469	199	0.470	0.444	0.475	1101
9	GLIS3	4289050	rs7034200	C	A	C	1092	2206	180	912	378	1828	60	78	51	225	466	223	0.495	0.476	0.499	1103
9	GLIS3	4293150	rs10814916	A	C	A	1043	2194	171	872	378	1816	63	81	45	234	476	198	0.475	0.452	0.480	1097
9	CDKN2B	22134095	rs10811661	T	C	C	423	2188	73	350	374	1814	122	57	8	592	280	35	0.193	0.195	0.193	1094
9	SARDH	133734024	rs573904	C	T	T	626	2206	120	506	378	1828	85	88	16	479	364	71	0.284	0.317	0.277	1103
10	CDC123	12265895	rs11257655	C	T	T	503	2208	93	410	378	1830	107	71	11	545	330	40	0.228	0.246	0.224	1104
10	CDC123	12286011	rs12779790	A	G	G	433	2208	78	355	378	1830	120	60	9	587	301	27	0.196	0.206	0.194	1104
10	CUBN	17114152	rs1801222	A	G	A	607	2198	114	493	376	1822	90	82	16	488	353	70	0.276	0.303	0.271	1099
10	HKDC1	69223185	rs4746822	C	T	C	968	2204	161	807	378	1826	60	97	32	276	467	170	0.439	0.426	0.442	1102
10	HHEX	92722319	rs7923866	C	T	T	783	2206	132	651	378	1828	75	96	18	374	429	111	0.355	0.349	0.356	1103
10	ADRA2A	111282335	rs10885122	T	G	T	292	2206	48	244	376	1830	144	40	4	687	212	16	0.132	0.128	0.133	1103
10	TCF7L2	112994312	rs34872471	T	C	C	759	2208	140	619	378	1830	72	94	23	394	423	98	0.344	0.370	0.338	1104
10	TCF7L2	112996282	rs4506565	A	T	T	819	2204	147	672	378	1826	68	95	26	356	442	115	0.372	0.389	0.368	1102
10	TCF7L2	112998590	rs7903146	C	T	T	774	2206	144	630	378	1828	73	88	28	387	424	103	0.351	0.381	0.345	1103
11	DUSP8	1675619	rs2334499	C	T	T	967	2180	172	795	376	1804	50	104	34	279	451	172	0.444	0.457	0.441	1090
11	KCNJ11	17387083	rs5215	C	T	C	772	2200	146	626	376	1824	66	98	24	396	406	110	0.351	0.388	0.343	1100
11	CRY2	45851540	rs11605924	A	C	C	1096	2208	178	918	378	1830	52	96	41	238	436	241	0.496	0.471	0.502	1104
11	MADD	47314769	rs7944584	A	T	T	711	2204	110	601	378	1826	92	84	13	412	401	100	0.323	0.291	0.329	1102
11	OR4S1	48311808	rs1483121	G	A	A	340	2204	53	287	378	1826	139	47	3	640	259	14	0.154	0.140	0.157	1102
11	FADS1	61804006	rs174550	T	C	C	675	2196	118	557	378	1818	88	84	17	432	397	80	0.307	0.312	0.306	1098
11	ARAP1	72721940	rs11603334	G	A	A	283	2208	43	240	378	1830	149	37	3	691	208	16	0.128	0.114	0.131	1104
11	MTNR1B	92940662	rs1387153	C	T	T	646	2206	136	510	378	1828	75	92	22	470	378	66	0.293	0.360	0.279	1103
11	MTNR1B	92965261	rs10830962	C	G	G	935	2196	180	755	374	1822	47	100	40	310	447	154	0.426	0.481	0.414	1098
11	MTNR1B	92975544	rs10830963	C	G	G	607	2204	132	475	378	1826	78	90	21	504	343	66	0.275	0.349	0.260	1102
12	GLS2	56471554	rs2657879	A	G	G	473	2206	83	390	378	1828	113	69	7	568	302	44	0.214	0.220	0.213	1103
12	IGF1	102481791	rs35767	A	G	A	346	2202	54	292	378	1824	139	46	4	650	232	30	0.157	0.143	0.160	1101
12	HNF1A	121022883	rs7957197	T	A	A	464	2200	71	393	376	1824	125	55	8	560	311	41	0.211	0.189	0.215	1100
12	P2RX2	132465032	rs10747083	G	A	G	769	2206	130	639	378	1828	87	74	28	373	443	98	0.349	0.344	0.350	1103
13	PDX1	27917061	rs2293941	G	A	A	534	2204	103	431	378	1826	97	81	11	538	319	56	0.242	0.272	0.236	1102
13	KL	32980164	rs576674	G	A	G	504	2192	83	421	376	1816	112	69	7	524	347	37	0.230	0.221	0.232	1096
14	WARS	100372924	rs3783347	G	T	T	383	2208	53	330	378	1830	141	43	5	609	282	24	0.173	0.140	0.180	1104
15	C2CD4A	62090956	rs4502156	T	C	C	1011	2202	174	837	378	1824	57	90	42	264	459	189	0.459	0.460	0.459	1101
15	C2CD4B	62141763	rs11071657	A	G	G	875	2208	156	719	378	1830	61	100	28	328	455	132	0.396	0.413	0.393	1104
16	FTO	53767042	rs1421085	T	C	C	914	2204	149	765	376	1828	65	97	26	303	457	154	0.415	0.396	0.418	1102
16	FTO	53782363	rs8050136	C	A	A	896	2194	154	742	376	1818	66	90	32	317	442	150	0.408	0.410	0.408	1097
16	CTRB2	75211105	rs9921586	G	T	T	281	2208	47	234	378	1830	143	45	1	693	210	12	0.127	0.124	0.128	1104
17	GLP2R	9888058	rs17676067	T	C	C	598	2206	120	478	376	1830	90	76	22	498	356	61	0.271	0.319	0.261	1103
17	HNF1B	37738049	rs4430796	A	G	A	1009	2206	169	840	378	1828	63	83	43	269	450	195	0.457	0.447	0.460	1103
19	CILP2	19547663	rs16996148	G	T	T	171	2208	26	145	378	1830	163	26	0	774	137	4	0.077	0.069	0.079	1104
19	PEPD	33408159	rs731839	G	A	G	762	2196	136	626	376	1820	75	90	23	383	428	99	0.347	0.362	0.344	1098
19	GIPR	45693376	rs2302593	C	G	G	1082	2198	188	894	378	1820	43	104	42	235	456	219	0.492	0.497	0.491	1099
20	FOXA2	22578963	rs6048205	A	G	G	110	2208	10	100	378	1830	179	10	0	819	92	4	0.050	0.026	0.055	1104
20	TOP1	41115265	rs6072275	G	A	A	336	2206	54	282	378	1828	138	48	3	654	238	22	0.152	0.143	0.154	1103
20	ZHX3	41203988	rs17265513	T	C	C	406	2204	68	338	378	1826	127	56	6	609	270	34	0.184	0.180	0.185	1102
20	SLC17A9	62967547	rs3746750	A	G	A	759	2200	111	648	376	1824	94	77	17	362	452	98	0.345	0.295	0.355	1100
21	BACE2	41209710	rs737288	G	T	T	773	2188	130	643	374	1814	74	96	17	373	425	109	0.353	0.348	0.354	1094
21	BACE2	41211811	rs6517656	G	A	A	458	2208	78	380	378	1830	118	64	7	573	304	38	0.207	0.206	0.208	1104

Main characteristics of the variants for the Caucasian (CAU) ethnicity.

CHROM, Chromosome code; LOCUS, Locus/Gene; POS, Base-pair coordinate [GRCh38]; ID, Variant ID; REF, Reference allele; ALT, Alternate allele; A1, Counted allele in logistic regression; A1_CT, Total A1 allele count; ALLELE_CT, Allele observation count; A1_CASE_CT, A1 count in cases; A1_CTRL_CT, A1 count in controls; CASE_ALLELE_CT, Case allele observation count; CTRL_ALLELE_CT, Control allele observation count; CASE_NON_A1_CT, Case genotypes with 0 copies of A1; CASE_HET_A1_CT, Case genotypes with 1 copy of A1; CASE_HOM_A1_CT, Case genotypes with 2 copies of A1; CTRL_NON_A1_CT, Control genotypes with 0 copies of A1; CTRL_HET_A1_CT, Control genotypes with 1 copy of A1; CTRL_HOM_A1_CT, Control genotypes with 2 copies of A1; A1_FREQ, A1 allele frequency; A1_CASE_FREQ, A1 allele frequency in cases; A1_CTRL_FREQ, A1 allele frequency in controls; OBS_CT, Number of samples in the regression.